Mass Effect: An Unlikely Alliance
by bardsofliterature
Summary: Commander Shepard, Hero of the Citadel and first Human Spectre joins forces with the Assassin Desmond Miles to learn about the origins of their mutual enemy as well as the gifts they share.
1. Introduction

"You're sure you want to do this?"

"Yeah…Absolutely. Everything's permitted right?"

In 2157, humanity discovered it was not alone in the universe.

Thirty years later, they found a peaceful place among dozens of galactic species. But this idyllic future is overshadowed by a dark past: Reapers, a sentient race of machines responsible for cleansing the galaxy of all organic life every 50,000 years, are about to return. The leaders of this galaxy are paralyzed by indecision, unable to accept the legend of Reapers as fact. But one soldier has seen the legend come to life.

And now, the fate of the galaxy depends on him.

Alliance Military Archives

Status: Highly Classified

Dated: 12th February, 2186

(All information classified within this archived data has been deemed as restricted for reference or perusal. Prior permission is required from the presiding Admiral (Currently Admiral Hackett) to access the files.)

2186. A year that would be marked as the turning point for the future of every race in the galaxy. The Reapers began their invasion starting with Earth as their main point of attack. No one knew what the Reapers were and why they would strike with such a vindictive fury. But it didn't matter. No amount of debating or reasoning would banish the impending doom that the machines brought with them. The Reapers laid waste to humanity and to every other race, turning the fallen into mindless husks to be used as cannon fodder and as a form of psychological warfare against the helpless organics. Only one man was able to foresee the doom that the Reapers bought with them. This man was Commander Shepard. Gifted with the mind of an expert military tactician, the strength of a true warrior and with a determination for which he was well known for, the First Human Spectre embarked on the mission of learning more about the origins of the Reapers and the ways they could be stopped. Shepard was armed with the tactile memories and knowledge of the Protheans, an enigmatic race of aliens thought to be wiped out by the Reapers 50,000 years ago. These aliens left a series of clues for the next generation to use as a weapon against the Reapers. One such clue was a Prothean Beacon on Eden Prime which gave Shepard his memories. He must now learn more about his gift and its origins, while simultaneously struggling to unite the races of the galaxy together in their war against the Reapers. But the journey may not be exactly as how he supposed it to be.


	2. Chapter 1

Alliance Military Logs

Transcribed on 4th January 2186

Vessel Reg. No: SSV Normandy SR2 Stealth-Class prototype frigate.

Commanding Officer: Commander Shepard (Spectre Agent).

Compiled by: Modified Cerberus V.I, E.D.I (Enhanced Defense Intelligence).

Report Status: Highly Classified, Code Black.

Location: Alliance Scientific Research Station, Mars.

Commander Shepard, the hero of the Citadel, Savior of the Galaxy and the first Human Spectre was in a serious mess right now. With Cerberus Guardians and Troopers pushing up with heavy fire, it became impossible to hold out the fight against the troopers. He was running out of Thermal Clips and his Omni-tool had just lost power from the shield overload he got from sustaining heavy Cerberus fire. His squadmates, Liara T'Soni and Lieutenant Commander Ashley Williams were in worse shape than him, continuously having to expend ammo to defend their flanks. Liara, an accomplished Asari biotic, famed archeologist and Shepard's oldest friend, was able to fend off the incoming troops with her biotic assaults, but even she grew tired and felt weakened by the increased assault. With no choice at hand, Shepard decided to take the fight to the next level. "Ashley, I'm going to need to rewire your Omni-tool's power into mine…I will need the juice to power my attack."

"Roger that, performing an Omni-tool rewire Commander." She held out her arm. A yellowish-orange gauntlet of light emerged from her arm and began to produce bluish crackles of electricity that suddenly began to light up Shepard's Omni tool, giving him a surge of power. Shepard used this power to activate his cloaking mechanisms and stealthily dispatch his opponents. The attack was effective and it neutralized all of the opposing troopers. Shepard grimaced as the last trooper fell to his Omni-Blade. A prodigy student of the N7 Alliance Shadow Corps Academy in Brazil, Shepard was a skilled infiltrator who could easily dispatch a squad of armed targets in the same time an entire squadron of marines would use to clear the area of the targets. Shepard took great pride in his skill, but never the opportunity to gloat about it or use it for nefarious reasons. There was the time he aided Cerberus, the same enemy that once helped him out in the past but that was because he shared an enmity for the Collectors along with them. He wasn't sure if Cerberus had any specific reasons in order to go rogue, but he never trusted from the start itself.

"Shepard, the floor looks clean and there are no signs of removal or even destruction for that matter. Are you sure the vision you saw wasn't just a flashback from our fight with the Synthetic?" Liara questioned.

"I'm sure Liara; the vision told me that Cerberus came back for something besides the design of the Crucible. I cannot recall what it was they wanted. Let's just sweep the area and find out what they were looking for."

Shepard had been here to Mars a while before and fought Cerberus before. They managed to defeat the Cerberus Synthetic Dr. Core and prevent her from downloading the plans for the Crucible, a weapon supposedly constructed by the Protheans in order to wipe out the Reapers once and for all. The mission was a success, but it came with serious consequences, brutally assaulted Ashley and sent her into a comatose state before being shot dead by Shepard. Thankfully Ashley had recovered and was on her feet, fighting the Reapers as humanity's second Spectre. She volunteered to aid Shepard in his mission to follow him to Mars, in order to help him seek the answers to the vision he acquired from the beacon at Eden Prime. Besides professional and military reasons, Ashley also had personal reasons for accompanying Shepard to this mission. As Shepard's Fiancée, she was deeply concerned for his wellbeing and wanted to make sure he could have the company he needed in order to process his emotions and strength he needed to lead the fight. She couldn't understand his feelings and emotions about the vision, but she promised to stand by him till the end.

"Commander, we should head back into the Normandy. Maybe the data needs to be processed for clues. We all need a break anyway..."

"You're right Ash. Joker, we need a pickup to the Normandy. Can you make it quick?"

"Roger that Commander would you also like some fries with that?" Joker replied. Jeff "Joker" Moreau was the Helmsman of the Normandy. It was his job to ensure the functioning of the navigation systems of the Normandy and to organize transport pickups for Shepard and his squad. In spite of being a patient of the debilitating Vrolik's Syndrome, he never let his condition get in the way of his exemplary service and his nature for making cheap wisecracks at the expense of other people. Shepard and Joker were close friends and that was the reason he let his jokes slide.

"No, we don't need fries Joker. I'm sure the Mess Sergeant does a better job at cooking than you could. E.D.I could you run a surveillance check on the site and run diagnostics as to why Cerberus would return to the facility?"

"Certainly, Shepard." E.D.I replied. An Unshackled Artificial Intelligence crafted from the remains of the Reaper Sovereign and the rogue Alliance VI, E.D.I was designed to aid Shepard against the Collectors. After Shepard's eventual defection from Cerberus, she agreed to aid him in his fight against the Reapers and Cerberus. Being a synthetic herself, she faced distrust from her organic counterparts who feared that she would turn against them should she have a chance. But Commander Shepard trusted her, and that was enough for her to justify her reasons. In addition to being a massive treasure trove of knowledge, E.D.I could manifest her consciousness into the static body of Dr. Core to become a mobile hacking platform, capable of sabotaging enemy defenses and overloading their shields and healing systems to her advantage. She was a vital tool to Shepard's operation and Shepard made it known to her always, as a method of earning her trust and loyalty for the mission.

Shepard bid goodbye to his squadmates and proceeded towards the War Room of the Normandy. The mobile command center was a hub of operations ranging from basic military intelligence procurement to complex data recognition and analysis systems. A team of Alliance Cryptographers and Intelligence personnel manned the extranet terminals, filtering vital pieces of data and clearing out any Cerberus propaganda that appeared out over the extranet. In addition to the officers, the War Room was filled with military strategists who consulted with Shepard over certain military operations. Many of these leaders came from governments such as the Turian Hierarchy, the Salarian Union, the Krogan Warlords of Tuchanka, the Admiralty Board of the Quarian Migrant Fleet and many other diplomats from the homeworlds of the Elcor, the Hanar-Drell and the Volus. These leaders offered military and financial support to the Alliance in return for certain favours from Shepard or from the Alliance themselves. No sooner Shepard entered the War Room; he received a beep on his Omni-tool that signalled him to the CIC room. As he entered the room, he was greeted by Specialist Samantha Traynor.

"Hello Commander, sorry to disturb you at this time but you've received a priority transmission from Omega. The sender wishes to speak in private with you. Ill patch it through to your cabin terminal."

"Thanks Specialist, carry on." Shepard was confused. Why would someone from Omega want to talk to him in private? Then it dawned upon him. No one else other than Aria T'Loak would send him a private vid message from Omega. Aria was the Queen of Omega who ruled the station with a fist of steel…and biotics. Aria was well feared and respected in Omega. She relied on Shepard's help several times back in 2185 and even in 2186 as she used his expertise to regain Omega back from Cerberus. She repaid the favour by providing Shepard with a huge pirate fleet, three groups of mercenary soldiers and her own mound of Element zero and credits. Shepard wondered why Aria would need to talk to him now that she didn't need his help. As he turned on his cabin's extranet terminal the face of Aria came into view.

"Hello Shepard, You miss me?" Aria said with a condescending tone.

"Aria T'Loak, I'm surprised you called. Today isn't my birthday you know. Not that I don't appreciate the greeting."

"Save it. I'm here to repay your efforts back in Omega. Don't expect anything else instead"

"Alright then. What is it you intend to offer me?"

"Information. It's what I'm good at. My scouts picked up readings of a Cerberus Research vessel in the planet Ilos in the Refuge System. I understand you've been there before and travelled through the Conduit?"

"I have. How is that relevant? And what does Cerberus need with Ilos?"

"No clue. That is up to you to find out. Maybe seek the help of a certain friend you call the Shadow Broker?"

Shepard was dumbstruck. No one knew about the secret that the Shadow Broker, a mysterious individual with a penchant for gathering information from the most secretive of places, was in fact Liara herself. She revealed it to Shepard and used her identity to gather information and resources for Shepard in his fight against the Reapers. No one knew her identity and no one should for her own safety... but Aria knew. Aria always knows….

"Surprised? Well don't be. Dr. T'Soni revealed it herself to me. We've begun a …. "Mutually beneficial" business relationship with each other. She can help you out."

"Very well. Thanks Aria". He logged out of the terminal.

Shepard then proceeded to Liara's office. He noticed Liara on her terminal sorting files with Glyph, her V.I assistant. Liara noticed Shepard's entry and logged out of the terminal, getting up to greet him.

"Hello Shepard, What can I do for you?"

"Liara. You revealed to Aria your identity?"

"Yes I did. It was a necessary strategy to ensure that I could gain Aria as an ally. And don't worry. She wouldn't be stupid enough to reveal it. She knows what's at stake if she did."

"Alright. Aria told me about the situation on Ilos. What can you elaborate on it.?"

"Not much Shepard. My spies were only able to gather so much data. After piecing it together, I was able to deduce that Cerberus was after a certain artifact on Ilos"

"The Conduit?" Shepard asked.

"No. the Conduit was depowered a long time ago. This artifact was actually quite newer than that. What's surprising is that it isn't Prothean in nature, the readings show something else in its entirety."

"I see. Could it be a Reaper weapon?"

"I don't think so. This may seem odd…but the signatures are actually not very old. Radioactive dating suggests that it may be at least a few hundred years old."

"That's a surprise. Why would Cerberus want such an artifact?"

"I cannot ascertain from this data Shepard. We will have to land on Ilos. Get to the mine where Cerberus is still frantically looking for the artifact and recover it for analysis. I would like to warn you in advance that the system is filled with Reapers and Cerberus Vessels."

"Great. Just what we needed. Alright Liara we will head down there. E.D.I and Joker set a course for the Refuge system towards Ilos. Make sure to engage our stealth drives upon entry."

"Aye Aye Commander."

Shepard then exited the corridor. He made his way to the various sections of the Normandy chatting up with staff and with his squadmates Garrus Vakarian, an ex-Citadel Security agent. Tali Zorah vas Normandy, Admiral of the Migrant Fleet, James Vega, an Alliance Marine, Ashley Williams and many other members of his crew and squad. Talking to these individuals made him prepared and ready for his battle. As the ship headed towards the Sol Relay, Shepard braced himself for Ilos and the fierce battle he was going to have to fight against Cerberus for this unknown artifact. He wasn't sure what to expect from this artifact, but he was determined to prevent Cerberus from acquiring it at all costs.

End of Chapter 1

Author's note: (whew that was fun. Sorry for being late guys. But exams take a lot of time. Lol. Hope to be making more soon and finishing the story before New Year's. Thanks to the subscribers and to all the people encouraging me to make more. More will come soon. Add your opinions and do add anything you want added into the story I might take it into consideration and incorporate it if necessary. Be sure to forward it to your friends and other Fan fiction subscribers. This story is purely fictional and is not a part of the actual game plotline.)


	3. Chapter 2

Alliance Military Logs

Transcribed on 5th January 2186

Vessel Reg. No: SSV Normandy SR2 Stealth-Class prototype frigate.

Commanding Officer: Commander Shepard (Spectre Agent).

Compiled by: Modified Cerberus V.I, E.D.I (Enhanced Defense Intelligence).

Report Status: Highly Classified, Code Black.

Location: Refuge System, Exact Co-ordinates unknown.

_Shepard was in a forest. Dark, gloomy with no hope of freedom. A child no more than age 10 darted past him laughing and having the time of his life. Shepard recognized the child as the one he saw back in Earth. He realized he was in a dream. He chased the boy. The boy continued to run. Eventually the boy grew tired. Shepard was able to catch up to him. But before he could grab the boy, the boy exploded into a ball of flames. Shepard was filled with terror at this point. But then suddenly an eagle rose from the ashes, flying away. Shepard began to chase it. And then suddenly a three headed dog chased the eagle towards a forest of red and orange and then to a dead forest. The three headed dog saw Shepard, it reared to attack him. But then the eagle attacked the dog. He left a mark on the dog…. A mark that made it an outcast, a mark that seared red. Shepard tried make out the mark on the dog's body but the dog ran away. The eagle then returned to its nest in the dead forest where it cared for three golden eggs .One of the eggs hatched a beautiful woman made of pure golden light. "Find the eagle" she mentioned, "find the apples…it is your only hope". Then she disappeared in red flames as Shepard saw his greatest enemy, Harbinger set him on fire. "Your purpose is fulfilled Shepard. You are finished."_

Shepard woke up. The terrifying vision lingered in his memory, waking him up from sleep. He couldn't make out the meaning of this dream and the exact significance of it. Ashley and E.D.I helped him to analyze the dream by deducing that the three headed dog was Cerberus and the forest of Red and Orange could have been Mars. Their deductions were correct as the first part of Shepard's dream came into fruition. Yet they couldn't tell what the other parts meant. Ashley was asleep next to him. Shepard didn't want to wake her from her sleep. She was very tired from their mission at Mars and he didn't want to disturb her. He got dressed and headed down to the CIC.

"Hello Joker, What's our status?" Shepard asked.

"Successfully navigated the mass relay Commander. Stealth Drives engaged. Setting a course for Ilos."

"Roger that. Carry on Joker."

Within a few hours, the Normandy entered the orbit of Ilos. Shepard chose Liara to guide him across the Prothean dig site and Garrus because of his superior sniping skills and combat knowledge on Cerberus fighting tactics. The three suited up and carried their respective rifles and headed out to the fourth floor to receive a pickup from Lieutenant Steve Cortez, their resident Kodiak Shuttle pilot. The shuttle landed on Ilos, at a safe distance far away from Cerberus AA defenses and marauding patrols. Once the Shuttle reached the Normandy, Joker piloted the ship out of orbit in order to decrease Cerberus suspicion and make things simpler for Shepard and his squad. They would wait until he completed the mission, and called for pickup.

Meanwhile, Shepard, Garrus and Liara headed to the dig site where the artifact was located. Garrus made sure to mask their suit signatures with the help of E.D.I and Liara pointed out to certain paths which her spies used in order to avoid being seen by Cerberus patrols. Ilos in itself was a barren planet, filled with ruins of the forgotten Prothean Empire. But the ruins were infested with Cerberus Troopers, Guardians, Phantoms and the huge Atlases that searched every corner of the ruin to locate the artifact. Shepard and the squad managed to evade the Cerberus patrols and head to the dig site. Unfortunately one of the Phantoms spotted Liara heading towards the mine. A vicious fight broke out, with Shepard, Liara and Garrus holing up against the massive waves of Cerberus fighters. The Phantoms, elite soldiers of Cerberus with powerful blades, tried to displace Shepard's hiding spot, but Garrus was able to pick off a few with his Raptor. Liara used her Scorpion Pistol, coupled with biotics to stamp out the remaining Phantoms and Shepard engaged a few with his Omni-Blade. After the Phantoms were dead, the remaining began charging at the squad. Shepard and his squad took cover, combining their powers with their abilities to take out the remaining hostile forces. Liara held a few in her Stasis grip as Garrus picked them off with his Sniper Rifle. Shepard used his legendary Spectre training to take out a few units with a simple Phaeston rifle with under the protection of his Infiltrator Cloak. After a hard and lengthy battle, the squad neutralized the waves of Cerberus troopers and proceeded to head into the mine. Liara was badly wounded but Shepard managed to revive her with his Medi-Gel. The mine itself was filled with many Cerberus soldiers, but Shepard and the Garrus took out the incoming troops as Liara took a break and rested from her injuries. Finally they reached the interior chamber were the troopers had planted charges to detonate the pile of rubble blocking their entry into the repository.

"Shepard, you should detonate the charges. That way we can get in.", Garrus said after observing the explosives. Shepard set the timer and detonated the charges. The explosion cleared all the rubble out. The squad went in. What they saw inside was a sight that caused great surprise to everyone.

The Repository was huge, big enough to store a dreadnought. Shepard was surprised at how a mine so small in looks could have a storage facility so deep. The walls were covered in strange glyphs and symbols that could not be interpreted by the system translator. Garrus and Shepard were awed at the size of the repository which was filled with statues and murals of glyphs that were incomprehensible. Shepard noticed that some of the statues looked similar to the beacons he found on Eden Prime. They were depowered and just looked like ordinary stones to him. Liara however was the most awestruck of them all. She recognized the glyphs as Prothean in nature and asked her V.I Glyph to document them.

"E.D.I, can you patch in Javik and ask him to come here. We could use his help deciphering the glyphs." Shepard asked,

"Certainly", E.D.I. Javik was a crew member of the Normandy and an expert in Prothean knowledge himself. The irony was that Javik's knowledge of Prothean comes out from the fact that he is a Prothean himself, the last of his kind to be placed in cryo-stasis, in order to avenge the fallen Protheans and lead the fight to the Reapers. Javik was in Thessia at the time, fighting with the Asari Commandos against the Reapers. But upon receiving word from Commander Shepard, he arrived via vidcomm chat to Shepard's Omni-tool.

"Javik, take a look at the building. What do you think it is?"

"I am not quite sure. It does look like a Prothean Library of Archives but it is in disrepair…the beacons cannot be accessed by touch as they are depowered. It is as good as useless. I am afraid I cannot reveal its purpose without those beacons." Javik mentioned.

After Javik was awakened on Eden Prime, he provided a lot of insight on the life of Protheans as well as his intake on the way the Protheans fell in the last cycle. He also mentioned that Shepard's memories were gained from the beacon when he touched it, since Protheans transferred knowledge and memories via touch through beacons that stored information. Shepard reasoned that the repository would have had these many beacons as a result. However neither Javik nor Liara, both able to transfer knowledge via touch, weren't able to explain to him how a human like him could gain those abilities without having one since birth. However he didn't really care anymore about it. The visions helped him to prepare the galaxy against the Reapers and that was all that mattered to him.

"All right Javik, once you get back to the Normandy, we can show you more of these data files to seek your analysis. Shepard out."

Liara was still transfixed at the glyphs. She continued to chart them and make rough translations. She almost lost track of her surroundings and she didn't even notice that Shepard spoke to Javik.

"Liara, found anything so far?"

"Nothing yet, the glyphs act like a little puzzle that opens a certain Vault door. But I cannot find the door, leave alone crack the puzzle."

"E.D.I, can you figure out some pattern? I'm sending you the glyph puzzle sequence"

"Of course Shepard. Diverting processing power towards the code. Preparing decoding algorithm. WARNING. Cerberus Troops found entering the repository. Please hold the location while I perform decoding sequence on the door."

No sooner E.D.I finished her message. The Repository was assaulted with a barrage of smoke bombs. Two Atlases entered the room, opening heavy fire on the squad while several Centurions appeared into the room with the help of their mobile jetpacks. Shepard and his squad were pinned down to the ground. There was no way he or his squad could have engaged those troops with the Atlases firing cannons at them. He prayed for a miracle to occur. Just then he noticed that the entrance was shaky from the explosions. A well placed explosion to the beams would crumble the roof of the entrance, thereby disabling the soldiers and the mechs. Sensing Shepard's plan, Liara fired a singularity beam on the mechs, disabling them and the soldiers for a while. This provided Shepard with an opportunity. He dashed to the pillars and planted a sticky grenade in each one of them. Then he managed to dodge enemy fire and return to the hiding spot. Garrus then opened fire on the sticky grenades. The resulting explosion brought down the roof on the Atlases, disabling them and the troops and ensuring that Cerberus wouldn't be a problem for them.

"We sure won't be coming that way now Shepard." Garrus said with a smug look on his face.

"Just then E.D.I's voice came up on the console. "Data decoding is complete. I am able to hack open the door."

"Well done E.D.I"

"Thank you Shepard. I always work at optimal capacity"

"Alright guys. Let's go in. Check out the interior vault."

Shepard then headed inside the vault. Liara and Garrus went inside after him. The interior vault was an exquisite sight. It was filled with symbols which radiated an ethereal aura of light. In the centre of the vault was a huge metallic cabinet. It looked more like a locker but it also looked a lot like an Alliance-issue Military Coffin, save for the circuits and the weird symbols on it that were nothing similar to the ones in the repository.

"Here it is." Liara replied. "The artifact Cerberus wanted to acquire at all costs."

"You mean this storage cabinet." Garrus interjected.

"Perhaps it is a Storage Cabinet. But we shouldn't open it yet. E.D.I there seems to be some circuits on it. Can you do an analysis of the box and its contents?" Shepard asked with a curious look

"Yes Shepard, entering system…. Scan Complete."

"What did you find?"

"Shepard, you won't believe this but…..this isn't some storage cabinet….the circuits are far too old for it. This is a Cryogenic Stasis pod."

"What? What do you mean Cryogenic Stasis Pod?"

"The Pod contains a standard issue cooling unit with a gene preservation mechanism. I detect life signs inside the pod. The pod's technology is very rudimentary as it allowed me easy access. There's also another thing Shepard…. The pod…. It has a human male inside of it."

"Goddess, There's a living human inside that pod? No wonder Cerberus wanted that pod... he must have known something about the Protheans to preserve himself inside this ruin with a Prothean pod." Liara added.

"That's the catch Dr T'Soni. The pod's internal computer suggests that it was arrived on Ilos in the year 2016 and departed Earth in the year 2013 with the occupant inside cryosleep. The software indicates that it was manufactured by an organization that predates any known Alliance originated industry. Researching…researching… The Corporation's name was Abstergo Industries. Dissolved in 2034. It says that he was sent by the National Aeronautics and Space Administration, A science division of one of the Human Governments before the formation of the Systems Alliance. The rest is unknown." E.D.I replied with a very surprised tone in her voice.

"This is very strange." Shepard replied. "I remember learning in school that actual space travel wasn't invented up and until around 2100 A.D. I guess they didn't take this into account." "E.D.I can you open the pod?"

"I'm not sure if that's a good idea Shepard. We can't say if he is still sane or even fully functional. We should do more scans before we can confirm anything."

"Do it E.D.I. If he came this far then it's a possibility he has some answers about the Protheans and the Reapers. Maybe even the vision I always keep having all the time at night."

"Very well Shepard. Keep ready for any hostile behaviour." E.D.I then uploaded an override code from Shepard's Omni-tool into the pod. The pod slowly disengaged its life support systems and engaged restoration systems. She then disengaged the locks and opened the pod door.

What they saw was a terrifying sight at first. A man in his mid-twenties was strapped to the pod. His skin was gaunt and grey and he looked like he just came out of a deep freezer. His bones protruded out of his skin and he was being a blue liquid intravenously. As soon as the sensors inside the pod opened the cold air gushed out of the pod onto Shepard. The tubes suddenly fed a red liquid into the man... returning his color back inside of him and restoring him to a healthier state. Shepard and Garrus pulled the tubes out of him and shut down the system. The man slowly came to life, coughing out liquid from his lungs and dangling from the hands of the two. As his strength returned he got onto his feet. But upon seeing Garrus and Liara, he suddenly retreated back to the pod and pulled out a P99 Walther from one of the compartments.

"Get away from me….I don't know what you are or why I am hallucinating like this but don't come near me or I'll shoot." , the man yelled.

Shepard observed the man carefully. He wore a white hood with blue jeans. He had a few tattoos on his arm and on that arm he wore a leather gauntlet. His head was close-cropped and his skin tone was the same as Shepard's skin tone. He wielded a pistol on his hand but the suit V.I estimated its threat level at below 10%. An ancient weapon, he thought. The suits shields could easily deflect his pellet shot. He was surprised at how the man reacted upon seeing Garrus and Liara. But he realized soon enough that the man didn't know anything about aliens or even the First Contact War. He asked Liara and Garrus to retreat back and approached the man.

"Listen to me. My name is Commander Shepard. I'm from the Alliance Navy. You were asleep in the pod for about 173 years. A lot has changed since then. I can explain but you have to let me. Put the gun down."

The man looked at Shepard with a shocked look. He obviously didn't expect to be sleeping that long. He looked at the human. Perhaps he was sincere. He dropped the gun. Perhaps it was the cold that ruined the mechanism but the gun misfired at Shepard. Thankfully the kinetic barriers effortlessly bounced the bullet away. The man was dumbstruck but he apologized.

"Sorry I didn't mean to do that. Gun just lost control. How the hell did your armor block that?"

"It's alright. I understand. Stand down everyone." Garrus and Liara holstered their guns. "Suit shields. You've been asleep a long time. The life you once knew has passed a long time ago. Earth has entered a new era into the future. The governments you knew have united into a single coalition called the Systems Alliance. The world has passed into the Space Age and made great strides in technology as we learned how to use the Mass Relays to travel across the galaxy. We use FTL capable ships so Cryo-pods are no longer necessary. Eventually in our exploration we came across other extra-terrestrial life, we fought wars with some but eventually made alliances with them. The galaxy was at peace until the Reapers attacked. Now we are looking for ways to fight the Reapers. The Protheans left us a series of clues for us to fight the Reapers. We found your pod in one of their ruins. A terrorist organization, Cerberus wanted to capture you for your knowledge about the Protheans and your presence in a Prothean ruin. But we came to you first. I know that this is a lot to process at one moment but if you come with us I'm sure we can help you answer some of your questions."

"Yes alright…and this Cerberus you speak of…they couldn't get anything from me anyways. I came here myself to this uncharted planet to discover the ruins of the People that Came Before….these individuals you call the Protheans. I needed answers just like you Commander."

"Really? Then I guess we can help each other. But you'll have to trust my crew. Not all of them are human…. Garrus is a Turian and Liara is an Asari. There are many other diverse species of aliens in the Galaxy who are also fighting against the Reapers. I'll explain to you more about them once we get to my spaceship."

"Don't worry Commander…This is all a little weird to me but I always expected the world to be a little more Star Wars-y"

Shepard was confused, "Star what-y?"

"Star Wars…it's an old movie/lore series. Should be ancient for you guys. Not for me. Oh never mind. You wouldn't know about it anyway. So how were you able to talk to those aliens in that weird language?"

"Oh we all have language translators in our suits. We'll outfit you with one along with space-travel stims and eezo boosts to travel with less pain on a spaceship."

"Ok hope it doesn't hurt too much."

"The surgery won't hurt…a lot" The man wasn't amused. "What's your name by the way?" Shepard asked.

"My name? My name is …..Desmond Miles."

End of Chapter 2


	4. Chapter 3

Alliance Military Logs

Transcribed on 29th January 2186

Vessel Reg. No: SSV Normandy SR2 Stealth-Class prototype frigate.

Commanding Officer: Commander Shepard (Spectre Agent).

Compiled by: Modified Cerberus V.I, E.D.I (Enhanced Defense Intelligence).

Report Status: Highly Classified, Code Black.

Location: The Citadel, Widow System.

_Shepard...dark forest…child...Burning...Eagle…three headed dog…Lady… "You must find the apples._

_You must find the apples."_

_Must find….apples._

"_Your purpose is finished Shepard."_

Shepard woke up. The nightmares and the sudden awakenings had become a routine occurrence and Shepard was somewhat used to it, in fact he felt odd and lost if he ever did have a good night's sleep. He dragged himself to the elevator and made his way down to the Engineering Deck. Tali Zorah vas Normandy, Engineer Adams and Engineers Gabriela Daniels and Kenneth Donelly were present, performing simulated tests on the thermal emissions of the Normandy, training it to hold the energy emissions while engaged in stealth mode, just like a mother patiently trains her child to go potty training. Tali was the most enthusiastic and proactive of them all. Most Quarians were very skilled in technical modifications and machine improvements and Tali just happened to be the best of them all. The others were asleep on their chairs when Shepard arrived. Tali was the only one awake and on duty the whole time. Shepard didn't bother waking up the others; he knew they needed the rack time after working graveyard shifts on the Ilos operation. He decided to talk to Tali to help her pass the time.

"Hey Tali, how are you doing so far?" Shepard asked.

"I'm doing well Shepard…Did you have nightmares again?" She asked him.

"Yeah sort of." By this time everyone on the Normandy knew about Shepard's nightmares including Ashley. Some offered words of advice, some their support. Nothing seemed to work though.

"How's Desmond doing so far? You meet up with him yet?"

"Yeah I did. He is a very charming human. Just like you Shepard. We talked for a long time. He told me so much about life on Earth before the future. He was very eager to learn about the Quarians besides the vids we showed him. He seemed sympathetic to our cause but kind of supported the Geth too. I just hope he could stop screaming at night. It gets really scary sometimes."

"I know… it's just that he needs time to adapt…the changes can have an adverse effect on some humans sometimes. How are things on Rannoch?"

"The colonization efforts have gone through smoothly. The Geth have really helped us to start up and increase ship production. We've also revised certain elements in our history and our politics to accommodate the Geth and give them equal representation. It's hard to let bygones be bygones but it's not like we have a lot of options at hand."

"That's good Tali. I'll talk to you later." Shepard had managed to acquire Geth and Quarian forces by negotiating a tough truce between them against the Reapers. His thoughts turned towards Desmond though. The following days after their meeting on Ilos was filled with a massive set of activities designed to integrate Desmond into Alliance society. Firstly Desmond was examined by Dr. Karin Chakwas, an Alliance doctor and Dr. Mordin Solus, a fast talking Salarian geneticist and doctor. Both doctors conducted surgical procedures to return Desmond into his original health. Dr. Solus prescribed a human exercise routine for Desmond to regain his stamina and build resistance for space travel. After that was successful, they retrofitted him with basic gene tissue implants, vaccines and a standard issue translator, which allowed Desmond to speak to Dr. Solus freely. He was then put into combat simulation to gauge his abilities.

After the tests were concluded, Desmond and Shepard talked freely and openly about things for many days. Shepard told Desmond how humanity had progressed in technology after discovering a Prothean dig site on Mars in 2157. He also talked and briefed Desmond about the First Contact War, the Discovery of the Citadel and the various races that inhabited it. He talked about many other things that had to do with mass relays, The Citadel, Spectres, aliens, currency, The Alliance and much more. Finally he spoke about his own story in brief from his trials as a Spectre to his fight against Saren Arterius and the Geth to the realization of the Reapers and their true purpose. He also talked about his death and resurrection by Cerberus. He told Desmond about his fight against the Collectors and their true purpose behind the human abductions. He also talked about Cerberus, the terrorist organization that had pro-human ideals, yet were fighting a war to pursue their own greedy interests. He also spoke about the final war and the Reaper's attack on Earth. As well as the struggles he had to face uniting the galaxy against the Reapers. Once Shepard was done, he made Desmond read as much as he could about the galaxy, its inhabitants and its way of life. After all that was done, Desmond began his story. He talked about the Ones who Came Before who enslaved the human race with the Pieces of Eden, a tool that could control human beings. He talked about the huge war between them and the solar flare that wiped out the Ones and left the Pieces and some humans alive. He then talked about the intense secretive struggle between the Templars, a group of humans dedicated to enslaving the human race by means of the Pieces and the Assassins, a group of free-thinking individuals who fought the Templars in order to safeguard the freedoms of the common man. He talked about himself then, of how he was captured by Abstergo, a Templar company in disguise and forced to enter a supercomputer called the Animus. The Animus enabled a user to access and relive the memories of his or her ancestors and learn more about their past. Abstergo made him relive the life of his ancestor in the Crusades, the Assassin Altair ibn La Ahad in order to determine the locations to the various pieces of Eden. But he eventually escaped and went into hiding with the help of his Assassin friends Shaun Hastings, Rebecca Crane and Lucy Stillman. He then revisited his ancestor in the Renaissance, an Italian Assassin by the name of Ezio Auditore da Firenze in order to learn more about the Assassin order and about the origins of humanity, the Pieces of Eden and the Ones who Came Before. Unfortunately he was visited by Juno, one of the Ones who Came Before and forced to kill Lucy, who was later revealed to be a traitor and a Templar sleeper agent. Desmond then spoke about his experiences in the Black Room, and then his experiences with his British ancestor Haytham Kenway and the Native American Assassin, Ratonhnhake:ton (Connor Kenway) during the American Revolution. He then described about the Second Disaster, and the choice he made to follow Juno instead of Minerva, thereby sacrificing his life to protect humanity. Although humanity would never know of his sacrifice or the sacrifices of the Assassin Order, he would be remembered as a hero and a savior by the Assassins. Shepard took a long time to understand this, continuously going to the extranet to read as much as he could about ancient human history. Shepard continued to explain that after the end of the Second Disaster and the safety of humanity, Juno managed to erase the minds of the Templars, Assassins and humans alike and return the world as it was before. She also destroyed most of the Pieces of Eden, keeping a few for her survival. She knew that with the end of the Templars and Assassins, there wouldn't be any danger to them at all. After 15 years of watching humanity progress scientifically and morally, she ascertained that it was necessary for her to leave humans to progress by themselves. She decided to give Desmond a parting gift by resurrecting him back to life by sacrificing her life energy to restore his. Desmond mentioned that he rose from the cave and proceeded to head out towards Abstergo to find out if the future had changed as he hoped. After realizing that Abstergo was now reformed and filled with employees who once were Assassins or Templars, he decides to work there as a typist. He mentions how he regretted Shaun and Rebecca not knowing anything about him at all but he realizes it was for the best. Later on as Abstergo began accepting volunteers for its Space program, the memories of Juno manifested inside of him, telling him to apply and to head towards the uncharted planet, to learn more about the origins of the Ones, the Pieces of Eden and a threat that would claim humanity in the near future, far more relentless and dangerous than the Second Disaster. He decided to learn to seek answers by applying, getting a cryo pod and a ship and reprogramming the ship's co-ordinates, thereby disappearing forever from the eyes of humanity. However the long ride had forced him into a cryo-sleep much longer than he expected and he ended up landing on the planet, still in cryo sleep, waiting until the day someone would arrive and free him.

After stories were shared and conversations made, Shepard took Desmond to the Alliance Armory on the Citadel. They decided to retrofit him with a N7 Shadow Infiltrator designation as he passed the fitness and combat requirements required for the position and was given special recommendation by the Spectre himself. They then introduced him to the Council, Admirals Hackett and Anderson and several other dignitaries. For the sake of his safety, his history was kept confidential under Citadel law and known only to select people. Admiral Hackett and Anderson were especially interested in his story since it was one that was never known in their history textbooks. They were especially surprised to hear about the Pieces of Eden, the Ones and the Assassins. Soon after all introductions were made, Desmond and Shepard both entered the Spectre Offices along with Ashley in order to pick a weapon for Desmond.

"So what are you going to choose, assault rifle, shotgun or sniper rifle?" Shepard asked.

"Ooh better yet, get loads of tech and biotic implants …those would be useful" Ashley added.

Desmond was confused. He rarely used a gun before, not even the P99 they had on display aboard the Normandy's Armory as a trophy. He looked at the hidden blade that was on display too. He couldn't use steel hidden blades as they were old fashioned and the rifles in the armory were too heavy, too tough or too slow to reload. He gave up hope and slouched in a corner. Just he noticed a video Shepard was watching alongside Ashley of him fighting Phantoms with an Omni blade and a cloak. He also noticed how the Phantoms cloaked themselves and use hand blasters to fight medium range foes. His mind lighted up as he thought of an idea.

"Shepard, I just got the most brilliant idea ever. Why don't you get me a Phantom outfit instead."

"Desmond, Cerberus is our enemy. If we start dancing around in their uniforms we might as well painted a red circle on our foreheads."

"I didn't mean an actual Phantom armor. I'm an Assassin: always was, always will be. I am a master of stealth killing. The Phantom's armor helps me to do just that. I can cloak and attack, I can use a wrist mounted Hornet instead of the Phantom's cannon and I can use dual Omni-Blades for melee combat, just like an actual Assassin would instead of those swords they have which can be shot off easily. What's best is that we can customize it into blue and black, the Alliance colors and add a hood instead of the Phantom helmet. How's that for creativity?"

"You know what? Normally I would think that's nuts, but somehow I actually think that's a good idea." Ashley added

"Yeah, in a way maybe the Assassins can be reborn to take the fight to the Reapers this time. After all Desmond, Nothing is true and Everything is Permitted. So you ready for this?" Shepard asked.

"Hell yes Shepard. Let's kick some Reaper Ass." Desmond said with a renewed confidence.

The design of the armor didn't take too long. Desmond's armor was made from the designs of the Cerberus Phantom and the N7 Shadow Infiltrator. It was blue with distinct shades of black. One patch of his breastplate was marked with the N7 insignia and the other patch was marked with the symbol of the Assassin order. His head was covered with a hood that generated its own shielding, protecting him from damage. He was outfitted with an Alliance issue Omni-tool with an additional customized Omni-tool on his other arm, both being able to generate high energy Omni-blades. This prototype was the first of its kind, designed to break barriers, shields and armor in a single hit and kill a target in a second hit. He was outfitted with a longer version of the Infiltrator's cloak, a prototype version which could store energy emissions into its shields allowing him to go for an hour without de-cloaking while regenerating shields, similar to the Normandy's design. These prototypes were meant to go into full effect, should Desmond become successful with them. His suit wrists were armed with customized Hornets on both arms that could spontaneously reload with the help of integrated virtual interfaces. Desmond now became an elite killer with the gear and skill that came close to rivalling Shepard himself.

After Desmond wore the armor, he and the rest returned to the Normandy, everyone was thrilled to meet him. Desmond retreated to the cargo hold where he looked at himself. Soon after Shepard came to the cargo hold to meet him.

"Hey, so how do you feel now?"

"I feel good Shepard. I feel I can return to my life again. I can seek the answers I always wanted. With your help we can get the answers I need. Maybe even use it to destroy the Reapers. Thanks Shepard, for finding me quickly before Cerberus did and for recognizing my talent and potential. And for allowing me to join you."

"I should thank you Desmond. You decided to continue the fight and help me fight the Reapers instead of giving up after losing so much in life. You are a true warrior."

"A man chooses his own destiny. Ezio once said that… maybe this was my destiny. I must reflect now. If you need my help be sure to call me."

"I will," and Shepard left the room. For he knew that on that day, the Reapers had one more adversary to deal with. Maybe they wouldn't win, maybe Desmond isn't the warrior he was once before. Maybe Shepard's nightmares would come true after all.

Then again Nothing's true and Everything is permitted.

End of Chapter 3

(Note: hope you liked it so far more to come in the future. Any aspiring artists... If you are interested in doing a Deviant art drawing of Desmond Miles as the N7 version of an Assassin, you can use my specifications to draw him for inspiration however should you think that another drawing would be good then feel free to draw that don't worry about copyrights or anything. I don't care about it… I would love to see your designs send it to me on your reviews and maybe I'll put it up in the ending. Also if someone draws Shepard or Femshep as an Assassin then I can put those up too. The best drawings/artwork will become the cover for the story. I'll need your permission too. Have a Merry Christmas everyone and continue to share this story with your friends on Fanfiction and outside of Fanfiction).


	5. Chapter 4

Alliance Military Logs

Transcribed on 4th February 2186

Vessel Reg. No: SSV Normandy SR2 Stealth-Class prototype frigate.

Commanding Officer: Commander Shepard (Spectre Agent).

Compiled by: Modified Cerberus V.I, E.D.I (Enhanced Defense Intelligence).

Report Status: Highly Classified, Code Black.

Location: Somewhere in the Widow System.

Commander Shepard looked into his extra-net terminal as he scanned the list of locations they needed to scout out for the Alliance to begin the War Effort and Ship Construction from. He went through the planets that were abundant in platinum and element zero as well as other useful materials. He also went through the planet dossiers, picking those with shipyards that were constructed for several corporations on the rich planets, but were subsequently abandoned by the owners after the threat of the Reapers became imminent. The task was getting increasingly strenuous and tiring, and the Commander was beginning to grow weary of all the paperwork that was still needed to be completed.

Then, his omni-tool came to life and buzzed with a familiar vibrating hum. Shepard tapped his omni-tool to answer the call. Desmond Miles's holoface stood at the other end of the line with an inquisitive look on his face.

"What's the matter, Desmond? You need anything right now?" Shepard asked.

"Yeah I do. I was going over the visions I saw and trying to analyze the meaning of them. It seems that the Ones who Came Before seemed to leave a lot of markers and symbols in an unknown location outside of Planet Earth. They also managed to replicate these glyphs in various other buildings, structures and locations on Earth to help them remember the location to this place. My guess would have to be that this location would have to contain a repository similar to the one my cryo-pod landed inside of that would actually be able to give us the tools required to find the truth about the origins of the First Ones."

"That's excellent." Shepard replied, "So why haven't you been able to find this repository yet?"

"That's the problem, I do not know why. A preliminary search of the extranet shows no resources with the said glyphs on them. It's like someone wanted it out of the extranet and underwent extra efforts to make sure it doesn't go back in."

"Yeah, I would presume either the Reapers managed to hide it from us or Cerberus is blocking out the information to ensure we remain in the dark. There is a solution to all of these problems though, Ill speak to Liara, the Shadow Broker and try to see if she can cook up something." Liara's position as the Shadow Broker ensured that she had control over every piece of information in the galaxy and that she was free of all the blocks most people would have in purveying information. Liara was able to circumvent the security networks of Cerberus, which in turn gave her classified information that she passed on to Shepard to help him strike at the base of their operations. Shepard was confident that Liara could find the information that Desmond needed to find the answers to the Protheans.

Shepard then headed down to the Crew Quarters, where Liara T'Soni's office was located. He saw that Desmond was already sitting in the Mess Hall, conversing with Garrus Vakarian, the Turian Ex C-Sec Agent and Shepard's oldest friend about the Turians as a species, their homeworld Palaven, their position in the galaxy and their morals and religious. Desmond was fascinated to hear Garrus talk about his people, how they placed others before themselves and focussed themselves on developing society than their own personal interests and how they valued discipline and strictness over everything else. Garrus also told him about the struggle in Palaven and the military support given to them by the Krogan, all thanks to the diplomatic efforts of Shepard in curing the genophage that the Krogan suffered from for several years. Upon noticing Shepard enter the entrance to Liara's office, Desmond ended his conversation with the Turian and joined Shepard to meet up with Liara. The two of them walked into Liara's office. Liara was in a conversation with one of her operatives, typing something that wasn't visible to them.

As soon as she noticed the two, Liara shut off her extra-net terminal and rose up to greet the two. "Shepard, Desmond…nice to see you around. I presume you're here today to find out the results for my search?" she inquired.

"Yes, Dr.T'Soni. We were hoping that your network of information specialists could help us retrieve the site where the glyphs could possibly be." Desmond replied.

"Yes of course. And please, you may call me Liara. I really don't mind."

"Very well Liara. Have you procured any information about the glyphs and their alternate locations?"

"Yes I have. Based on the diagrams you gave me, I ran a full diagnostic scan of any digsites or planets with research centres where a similar set of patterns were noticed in their results. It took a long time and a lot of digging to recover the information but I was able to fine-tune the results down to two sites. I was able to pinpoint two Prothean digsites that contained research data with symbols similar to the glyphs you just traced out. I confirmed these locations to be Gei Hinnom in the Sheol System and Feros in the Theseus System."

"Hold on Liara, did you just mention that the glyphs Desmond saw in his vision were seen at a Prothean digsite? Do you think the Protheans were in reality the Ones who Came Before who triggered all of this?" Shepard asked.

"I can't say for sure Shepard. Desmond mentioned that the Ones who Came Before were technologically advanced and tried to control humanity before they vanished. While this does tempt us to assume that the Protheans were the Ones and that their attempts to control humanity were cut short by the Reaper attack, I can't really confirm for sure. However as an archeologist and optimist I am very curious to find out more about the Prothean involvement in human evolution. We know for a fact that the research facility on Mars was built in order to examine and study humans and Javik himself mentioned that the Protheans tried to colonize and prepare the younger races of the galaxy in order to prepare them for the future but I can't really speculate anything without good reason. Our best course of action would be to head to Gei Hinnom and begin searching the Prothean ruins in there for more answers. Feros is not an option as this moment as it is surrounded with Reapers. But we can find more answers in Gei Hinnom."

"I see. Very well, Joker, E.D.I set a course for the Sheol System and specifically Gei Hinnom. We need to get there as soon as possible."

"Roger that Commander, preparing to exit Widow Relay in 5…4…3…2…1… FTL jump successful. All systems are at 100%, stealth drives engaged. We are now heading towards the Sheol System."

No sooner Joker finished his message, E.D.I appeared at the console.

"Warning. Warning. Two ships located on the ladar. Now shifting to intercept trajectory."

"Who are they E.D.I, Reaper Destroyers or Pirates?" Shepard asked as he rushed towards the cockpit.

"Negative. Ship bears signatures bearing the standard frequency of the Quarian Migrant Fleet. Preparing to slow ship down and hail the allying ships. Do I have your permission to do so?"

"Roger that E.D.I, send in a quick message but remain on your guard. Just because they are Quarian ships doesn't mean they have to have Quarian personnel on them. Prepare to launch countermeasures if necessary and call Tali here to the cockpit as soon as possible."

"Of course Commander." Shepard had reached the cockpit already by then. He looked out of the pilot's window to notice two cruisers heading towards the Normandy. Although they were well armed and capable of taking down the Normandy in a few shots, they stayed clear and adopted a more defensive stance against the Normandy. Shepard thought they did so in order to avoid confrontation with a ship belonging to the Systems Alliance; however they weren't willing to take any risks letting them across. Soon enough the comm link popped up, a Quarian captain stood at the other end.

"Greetings, I'm Captain Nilas'Danna vas Zenithar of the Migrant Fleet. I speak for the crew of the Zenithar as well as the crew of the Hisochus. We are currently engaged in a series of skirmishes against pirates led by the Blood Pack faction. We received a distress call from an Alliance colonist who said that her colony on Gei Hinnom was attacked by Blood Pack mercenaries. As we were the closest to the system, we volunteered to evacuate the human colonists and repel the mercenaries. The Blood pack Carrier escaped but we feel they might return to get revenge. Please excuse our aggressive nature Captain; we just wanted to verify if your ship was indeed Alliance or Blood Pack."

"No problem Captain Nilas. I am Commander Shepard of the Alliance Navy and we are on a recon mission on Gei Hinnom to explore a Prothean Ruin. I have Admiral Tali'Zorah vas Normandy on board who will verify our claim. I will have my helmsman call in for Alliance Reinforcements as soon as possible."

"Of course Commander. We have received confirmation from Admiral Tali'Zorah. We have evacuated most of the citizens of the Alliance colonies. I'll have the Hisochus escort them through the relay into the Citadel." Once he was finished, the Hisochus broke formation and joined a group of other ships that were heading towards the system's Mass Relay. "We will stay behind and escort the last two ships that are supposed to evacuate in about five minutes or so." Admiral Nilas replied. "We should expect them to be quick about it Commander. Oh no… the Blood Pack Carrier has returned Commander. We need your help to handle it…it is the only way we can evacuate the citizens safely. Commander, if you could engage the carrier we would hurry up as soon as possible and evacuate the citizens to safety."

"Roger that Captain. Joker set our ship to attack course. E.D.I get your cyber warfare systems ready for attack. All Crew Members this is the Commander. Prepare for starship combat and proceed to battle stations. Brace for Collision."

The Normandy then broke formation and accelerated its thrusters towards the Blood Pack Carrier. The Carrier itself was larger than the Normandy and it looked just as fiercely armed. The Carrier suddenly beamed to life and opened fire at the Normandy. Waves of gunfire sped towards the Normandy, but thanks to the expert maneuvering of Joker and the Normandy's Cyclonic Barriers, the Normandy escaped the fire. The Carrier then unloaded a barrage of disruptor torpedoes one by one without a pause on the Normandy. Two of the torpedoes hit the starboard side and underside of the Normandy, damaging the shields.

"E.D.I, what's our damage report?" Shepard asked.

"Shield levels at 40%, Major damage to Armor Plating but otherwise no casualties in the starboard side or underside of ship deck." E.D.I replied.

"Alright E.D.I, launch ship to ship cyberwarfare attack. I want you to cripple their main targeting systems, Shielding and propulsion systems. Override and disable them. Joker, buy her some time to perform the necessary sabotage."

"Roger that Commander." E.D.I replied.

"Aye Commander." Joker responded.

As the Carrier continued to fire mercilessly on the Normandy, the Normandy evaded the Carrier's weapons and continued to flank the cruiser, firing its own arsenal in the process. Soon enough a message from the Zenithar popped up in the Commander's terminal.

"Commander Shepard, this is the Captain. All ships have been accounted for and all civilians have been rescued. We are now heading towards the mass relay. Thank you Commander."

"Roger that Captain. And thank you for helping our people out in need." Shepard replied.

"E.D.I what's your progress?" Shepard asked,

"I have gained entry into their systems. Performing overrides now."

No sooner E.D.I was finished, the Normandy fired a high powered EMP wave at the cruiser which self-detonated the Carrier's missile systems, shut off their main engines and essentially shut the Carrier down. Before the Blood pack realised what happened, it was too late to correct the systems. The Normandy then fired its own prototype Thanix Magnetic-Hydrodynamic Cannon at the Carrier. A Turian prototype created from the remains of the main gun of the Reaper Sovereign, the Carrier's armor was no match for the cannon, which easily tore through the ship's shielding and armor and destroyed the ship completely.

"Yeah! How do you like that you little turds?" Joker yelled with excitement.

"Well done E.D.I." Shepard replied. "And you too Joker."

"Thank you Shepard. I always work at optimal capacity." E.D.I replied confidently.

"What's our Damage report at E.D.I?"

"Ship's shields are at 30%. No major damages, no casualties. Our arsenal has been lightly depleted but we can rearm, repair and refuel at the Relay's repair ship." E.D.I replied.

"Uhh… Commander take a look… we have three Dropships exiting the destroyed Carrier towards the surface of Gei Hinnom. The radiation signatures are excessively high in one of those dropships. E.D.I can you run a scan on the ships for me." Joker asked in a cautious tone.

"Certainly Joker. Performing Scans… you were correct Joker… the radiation levels on the dropship was significantly higher than usual. Shepard if my scans are correct, the Blood Pack are deploying a powerful thermo-nuclear bomb on the planet's surface." E.D.I replied with a hint of hesitation in her tone. "Estimated point of arrival is three clicks north of the digsite."

"They're planning to blow up the digsite. Somebody must have hired them to blow up the digsite. Most probably Cerberus." Shepard replied.

"Commander you need to go down there, and stop them from blowing up the place." Joker replied. "I'll ready a dropship for you."

Shepard wasn't going to argue. He hurried to the hangar where James Vega, Liara T'Soni, Ashley Williams and Desmond Miles stood, geared up and ready to go. Tali'Zorah joined them too. Garrus decided to stay on deck and co-ordinate the team ahead. The company was split in groups of two with Desmond, Shepard and Liara on one group and Tali, James and Ashley in another.

"Finally, I get to kick some Krogan ass..." James said with a smug look.

"Roger that. But you stick with Ashley nonetheless and follow her orders." Shepard replied. To which James gave a nod.

"Take care of yourself Shepard." Ashley said with concern in her voice.

"Yes, I will. You be sure to come back to me safe and sound too." Shepard replied.

The groups then took two individual dropships towards the digsite. The plan was to drop in and for one group to engage the enemy while the others try to defuse the bomb. Shepard and his squad would take out the enemy Blood Pack while Ashley's squad would try to defuse the bomb. Tali being the most technologically advanced of the latter, could easily defuse the bomb while the other two covered her. Shepard also decided to enter the digsite to find out more while the other squad defended him. As they flew towards the digsite, Shepard noticed Desmond sitting in a corner, with a calm look on his face.

"How are you feeling Desmond? You think you can handle the Blood Pack troopers?" Shepard asked with genuine concern.

"I'm alright… I've read a lot about the Krogan and Vorcha and their fighting styles… I think I can manage them. What I'm thinking about are the Protheans… could they have really been our ancestors. Were we just living a lie all this time around?" Desmond asked.

"I don't know… once we reach the digsite all the truth will be revealed…" Shepard replied.

"Yeah I sure hope so…" Desmond replied with a glum tone…

Their journey wasn't going to be an easy one….but it would sure be a unique one.

(Author's note: I apologize for the delay….combination of the flu, school, work and exams really took a toll. I will try to get it done soon.)


End file.
